Clients for Biological Database Web Services

Documentation for package ‘bioclients’ version 0.1.1

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-- A --

alphafold_model	The predicted structure for a UniProt accession
alphafold_parse_model	Turn an AlphaFold prediction response into a table

-- C --

civic_gene	Curated clinical evidence counts for a gene
civic_parse_gene	Turn a CIViC gene response into a table
clingen_alleles	Resolve HGVS to canonical allele ids
clingen_gene_validity	The ClinGen gene-disease validity table
clingen_parse_allele	Turn one Allele Registry element into a table row
clingen_parse_batch	Turn an Allele Registry batch response into a table
clingen_parse_validity	Parse the ClinGen gene-validity CSV
clingen_validity_for	Filter a parsed validity table to one or more genes
clinvar_category	Bucket a ClinVar significance string into a coarse category
clinvar_classification	Look up the ClinVar classification for a variant
clinvar_conditions	Collapse a ClinVar trait set into one condition string
clinvar_parse_record	Turn a ClinVar esummary record into a table

-- D --

dgidb_gene	Drug-gene interaction count for one gene
dgidb_genes	Drug-gene interaction counts for many genes
dgidb_parse_genes	Turn a DGIdb genes response into a table
diseases_channel	Genes DISEASES associates with a disease, from one channel
diseases_gene_associations	Genes DISEASES associates with a disease, across both channels
diseases_merge_channels	Combine DISEASES channels, keeping the strongest score per gene
diseases_parse_channel	Turn one DISEASES channel response into a table

-- E --

ensembl_gene_model	The exon model for a gene
ensembl_parse_consequences	Turn Ensembl transcript consequences into a table
ensembl_parse_gene_model	Turn an Ensembl gene lookup into a gene model
ensembl_parse_vep	Turn an Ensembl VEP record into a result
ensembl_vep_id	Run VEP for a variant id
europepmc_count	How many publications Europe PMC has for a query
europepmc_parse_count	Read the hit count off a Europe PMC response
europepmc_parse_results	Turn Europe PMC search results into a table
europepmc_query	Build a Europe PMC query from terms
europepmc_search	Search Europe PMC

-- G --

gnomad_constraint	Gene constraint for one gene
gnomad_constraints	Gene constraint for many genes
gnomad_frequencies	Population allele frequency for many variants
gnomad_frequency	Population allele frequency for a variant
gnomad_frequency_by_id	Population allele frequency for a variant, by id
gnomad_parse_constraint	Turn a gnomAD constraint response into a table
gnomad_parse_constraints	Turn an aliased gnomAD constraint response into a table
gnomad_parse_frequency	Turn a gnomAD variant response into a frequency record
gnomad_parse_populations	Combine gnomAD per-ancestry counts into one frequency table
gnomad_parse_variant	Turn a gnomAD variant response into a frequency row
gnomad_parse_variants	Turn an aliased gnomAD variant response into a table
gnomad_variant_id	Build a gnomAD variant id from variant components
gtex_gene_reference	Resolve a gene to GTEx's versioned GENCODE id
gtex_median_expression	Median expression across tissues
gtex_parse_expression	Turn a GTEx median-expression response into a table
gtex_parse_reference	Turn a GTEx gene-reference response into a table

-- H --

hpa_gene	The Human Protein Atlas record for a gene
hpa_parse_gene	Turn an HPA gene record into a table
hpo_gene_annotation	HPO's annotation for a gene
hpo_parse_diseases	Turn an HPO gene annotation into a table of diseases
hpo_parse_phenotypes	Turn an HPO gene annotation into a table of phenotypes
hpo_parse_search	Turn an HPO search response into a table
hpo_parse_term	Turn an HPO term response into a table
hpo_search	Search HPO terms by free text
hpo_term	Resolve one HP id to its term

-- I --

impc_gene_phenotypes	Significant knockout phenotypes IMPC records for a human gene
impc_mouse_ortholog	The mouse ortholog IMPC holds for a human gene
impc_parse_ortholog	Read the mouse ortholog out of an IMPC gene-core response
impc_parse_phenotypes	Turn an IMPC phenotype response into a table

-- M --

monarch_associations	Associations with an entity on one end
monarch_gene_phenotypes	HPO phenotypes Monarch associates with a gene
monarch_hgnc_id	Normalise an HGNC id to the CURIE form Monarch expects
monarch_parse_associations	Turn Monarch association records into a table
monarch_parse_search	Turn a Monarch search response into a table
monarch_search	Search Monarch for an entity
mygene_gene	Look up one gene
mygene_genes	Look up many genes in one request
mygene_parse_batch	Turn a MyGene batch response into a gene table
mygene_parse_hits	Turn MyGene hits into a gene table
mygene_pick_hit	Choose the best MyGene hit for a queried token
myvariant_id	Build a MyVariant identifier from variant components
myvariant_parse_batch	Turn a MyVariant batch response into a table
myvariant_parse_record	Turn one MyVariant record into a table row
myvariant_variants	Annotate many variants in one request

-- O --

opentargets_disease_targets	Genes associated with a disease
opentargets_drugs	Known drugs and clinical candidates for a gene
opentargets_gene_diseases	Diseases associated with a gene
opentargets_is_id	Is a term an ontology id rather than free text
opentargets_parse_diseases	Turn target-to-disease rows into a table
opentargets_parse_drugs	Turn known-drug rows into a table
opentargets_parse_matches	Turn a disease search or lookup into a table
opentargets_parse_pgx	Turn pharmacogenomics rows into a table
opentargets_parse_targets	Turn disease-to-target rows into a table
opentargets_pgx	Pharmacogenomics annotations for a gene
opentargets_resolve_disease	Resolve a disease term to ontology records

-- P --

panelapp_all_panels	The whole PanelApp panel index
panelapp_panel	The genes on one PanelApp panel
panelapp_panels	One page of the PanelApp panel index
panelapp_parse_index	Turn a PanelApp panel index page into a table
panelapp_parse_panel	Turn a PanelApp panel detail into a table of genes
pdbe_parse_structures	Turn a PDBe best-structures response into a table
pdbe_structures	Experimental structures for a UniProt accession
pharos_parse_targets	Turn a Pharos targets response into a table
pharos_target	Target Development Level for one gene
pharos_targets	Target Development Level for many genes
protvar_function	Functional context for a residue
protvar_parse_function	Turn a ProtVar function response into its text
protvar_parse_population	Turn a ProtVar population response into a table
protvar_population	Known variants at a residue
protvar_position	Pull a residue position out of a protein-change string
protvar_strip_citations	Strip inline citations out of a UniProt function comment
pubtator_entity	Build the PubTator3 entity token for a gene
pubtator_gene_literature	Articles PubTator3 has tagged with a gene
pubtator_parse_count	Read the article count off a PubTator3 search response
pubtator_parse_results	Turn PubTator3 search results into a table

-- Q --

quickgo_annotations	GO annotations for a UniProt accession
quickgo_parse_annotations	Turn a QuickGO annotation response into a table

-- R --

reactome_parse_pathways	Turn a Reactome pathway array into a table
reactome_pathways	Reactome pathways for a gene symbol

-- S --

string_map_ids	The STRING identifier map for a set of symbols
string_network	The interaction network within a set of genes
string_parse_ids	Turn a STRING identifier-map response into a table
string_parse_network	Turn a STRING network response into an edge table
string_parse_partners	Turn STRING interaction-partner rows into a table
string_partners	Interaction partners for one gene
string_reconcile_edges	Rewrite edge endpoints back into the queried symbol space

-- U --

uniprot_diseases	Diseases UniProt curates for an accession
uniprot_features	Sequence features for an accession
uniprot_features_at	The features spanning a residue position
uniprot_parse_diseases	Turn a UniProtKB entry into a curated-disease table
uniprot_parse_features	Turn an EBI Proteins features response into a table

-- V --

variantvalidator_normalize	Validate and normalize one HGVS variant
variantvalidator_parse	Turn a VariantValidator response into a table
vep_default_options	The request flags VEP is asked for by default
vep_default_throttle	The default rate limit for VEP requests
vep_key	Build the variant key VEP results are matched on
vep_parse_batch	Turn a VEP batch response into a table
vep_parse_colocated	Turn the colocated variants of a VEP element into a table row
vep_parse_element	Turn one VEP element into a table row
vep_pick_transcript	Choose which transcript to report for a variant
vep_region	Build a VEP region string from variant components
vep_variants	Consequence predictions for many variants
vep_variants_all	Consequence predictions for any number of variants